Keith,
What is your current carb setup? 123 mains, what pilots, needles - stock, TBS or Thruxton? Snorkels out? How many turns out on your idle screws?
My gut feel is that you are running lean. I have virtually the same bike and I'm running long straight through TORS with no snorkels, the intake where the snorkel seats has been beveled and opened up to max size. I needed to increase my mains to 135 but also installed TBS needles and have 42 pilots. I plan to install 45 pilots and try reducing the mains to 130s but hesitate to do so because the bikes pulls so well. My bike was sluggish when I replaced the filter especially after pulling the snorkels. You'll sort it out. BTW, my bike pulled hard even with the valves out of adjustment, mind you they were all loose.
Here is a seat of the pants test to check for proper main jet size. On a long straight (free from the local police), wind the bike out in 4th or 5th. Get it above 5000rpms accelerating hard and then slightly back off the throttle. If the bike seems to pick up speed, your mains are too small. The opposite, too big. Nothing and you are just right.
